[Freesurfer] Extract peak voxel (vertex) coordinates from surfaces

Dear Freesurfers, I would be interested in figuring out the peak vertex of clusters based on coregistered functional FEAT data with the reconstructed anatomical surfaces. The FEAT preprocessing was run without smoothing and smoothing was applied after the feat2surf Does anyone know how to

[Freesurfer] Longitudinal Pipeline for Subjects with only 1 assessment

Dear FS Experts, I am running a longitudinal analyses, and I'd like to use the Linear Mixed Effect framework as even subjects with only 1 time-point can be included into the model. How do I create the base for a subject with only 1 TP? Is this the correct approach? recon-all -base *[basename]*

Re: [Freesurfer] Longitudinal Pipeline for Subjects with only 1 assessment

Hi Elijah, the recon-all command is correct. The error you are getting is something else. Does the ribbon file exist? I would re-run that base from scratch, could be an IO problem or disc space etc. Martin On 05/30/2014 08:56 AM, Elijah Mak wrote: Dear FS Experts, I am running a

Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal

Thanks for the tip. Another question. In the dmrirc file, can we also define multiple bval file? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you Yoon On May 22,

[Freesurfer] Seg fault

Hi, I've been working with Freesurfer for years and have suddenly been getting this fault: tkmedit started: Fri May 30 10:08:23 2014 /Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz -aux T1.mgz -surfs $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name:

Re: [Freesurfer] Seg fault

Thanks for the quick responses. I'm using version 10.7.5 - I purposely haven't updated this as we've been analysing a large set of intervention data. I'm also using freesurfer-Darwin-lion-stable-pub-v5.3.0 - again we've been consistent with this and have run everything in this version. I'm still

Re: [Freesurfer] Seg fault

It might be the data you are trying to load in. Does it happen with other subjects or volumes? On 05/30/2014 12:17 PM, Cooke, Gillian wrote: Thanks for the quick responses. I'm using version 10.7.5 - I purposely haven't updated this as we've been analysing a large set of intervention data.

[Freesurfer] creating norm.mgz

Hi all, I'm trying to use tkmedit to pick electrode points for a patient. For the mri, I'm using the average brain provided by freesurfer. I realized that I have no norm.mgz file which tkmedit calls. How do I create this? Thanks, Mia ___ Freesurfer

Re: [Freesurfer] creating norm.mgz

why not just use the orig.mgz that is there? On 05/30/2014 02:40 PM, Borzello, Mia wrote: Hi all, I'm trying to use tkmedit to pick electrode points for a patient. For the mri, I'm using the average brain provided by freesurfer. I realized that I have no norm.mgz file which tkmedit calls.

Re: [Freesurfer] Registration of Functional Data to the Inflated Brain

Thanks Bruce. The problem is that the registration itself is not working properly. Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding

Re: [Freesurfer] Registration of Functional Data to the Inflated Brain

Hi Sherryse mostly I'll leave this for Doug. Have you tried using bbregister directly? It might be embedded within reg-feat2anat, I'm not sure Bruce On Fri, 30 May 2014, Sherryse Corrow wrote: Thanks Bruce. The problem is that the registration itself is not working properly. Recap: The

[Freesurfer] meshes/surfaces for sub-cortical structures

Hi Freesurfers, I'm wondering whether the meshes (list of vertices+faces) corresponding to structures such as the hippocampus and amigdala are available as part of the Freesurfer output? In the /surf folder there are only the meshes of whole brain structures (cortex, pial, WM...). Is there any

Re: [Freesurfer] meshes/surfaces for sub-cortical structures

sure, you could use mri_tesselate or mri_mc for this. We don't typically generate them as the structures don't really have a surface-based organization so (for example) interior points aren't represented on the mesh On Fri, 30 May 2014, Tanya wrote: Hi Freesurfers,I'm wondering whether the

Re: [Freesurfer] Control point error

Hi Victor, This recon was originally processed with FS5.3, but when you reran it with autorecon2-cp -autorecon3 you used FS5.1. Could you try rerunning this case again with the same (314) control points using FS5.3 instead and see if the right frontal area of the wm surface is severely

Re: [Freesurfer] creating norm.mgz

Right that will work. I will try that. Also in using the average brain am I able to compute the pial layers(lh.pial-outer-smoothed, rh.pial-outer-smoothed)? I tried and it errored- i attached a screenshot of the error. Thanks a lot, m From:

Re: [Freesurfer] creating norm.mgz

Or is there a file that corresponds to the outer-smoothed pials? like lh.pial_avg or lh.pial.avg.area.mgh that I can use? Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve